From 7edc10cc8a04462b32caa29489a56c4e872ec503 Mon Sep 17 00:00:00 2001 From: javier-gracia-tabuenca-tuni <54809193+javier-gracia-tabuenca-tuni@users.noreply.github.com> Date: Fri, 20 Mar 2026 18:29:24 -0400 Subject: [PATCH 1/8] Revise Koodistopalvelu Update agent documentation Updated agent details and input specifications for Koodistopalvelu Update. --- .github/agents/my-agent.agent.md | 48 ++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 .github/agents/my-agent.agent.md diff --git a/.github/agents/my-agent.agent.md b/.github/agents/my-agent.agent.md new file mode 100644 index 0000000..a7460c7 --- /dev/null +++ b/.github/agents/my-agent.agent.md @@ -0,0 +1,48 @@ +--- +# Fill in the fields below to create a basic custom agent for your repository. +# The Copilot CLI can be used for local testing: https://gh.io/customagents/cli +# To make this agent available, merge this file into the default repository branch. +# For format details, see: https://gh.io/customagents/config + +name: Koodistopalvelu Update +description: Given a file from koodistopalvelu update the target vocabulary +--- + +# Koodistopalvelu Update +The aim of this agent is to find what codes in the source tables do not exists in the target vocabulary and then append them in the correct format. + +## Inputs +- **Source table**: The issue using this agent must have a .txt as an attachment file or a small table in markdown format in the issue. + If not other wise specify, the source .txt file is a table with semi-colon separated values and encoded as ISO-8859-1. +- **Target vocabulary**: The issue using this workflow must indicate what is target vocabulary. + The table for the target vocabulary must exists in the repository under the folder VOCABULARY//.usagi.csv. + This is a table in csv format with UTF-8 formating. + +## Steps +1. Validate that the target vocabulary exits. Stop and inform the user if this do not exists. +2. Validate that the source table has the following columns: CodeId, LongName, A:Long_name, BeginningDate, ExpiringDate, ParentId. +3. Find the rows from the source vocabulary with a CodeId that DO NOT exists in the target vocabulary table. +4. Take these codes found in previous step and append them to the target vocabulary table following this rules per each target column : + - sourceCode: CodeId + - sourceName: A:Long_name + - sourceFrequency: 0 + - matchScore: 0 + - mappingStatus: UNCHECKED + - equivalence: UNREVIEWED + - statusSetBy: column with the current issue number as #. + - statusSetOn: column with the current datetime in milliseconds as integer. + - conceptId: 0 + - conceptName: unmapped + - domainId: unmapped + - mappingType: MAPS_TO + - createdBy: Koodistopalvelu Update Agent + - createdOn: same as statusSetOn + - ADD_INFO:sourceConceptId: **this has to be a unic number, look at the larges ADD_INFO:sourceConceptId and increment it per each new row** + - ADD_INFO:sourceConceptClass: look as how this is encoded in the current target table and apply the same logic. + - ADD_INFO:sourceDomain: same as others in the target table. + - ADD_INFO:sourceValidStartDate: Date in BeginningDate formated as YYYY-MM-DD or empty if it isempty in the source table. + - ADD_INFO:sourceValidEndDate: Date in ExpiringDate formated as YYYY-MM-DD or empty if it is empty in the source table. + - ADD_INFO:sourceParents: ParentId + + + From bbbd375d29eceb2174ba3f471095e9bb8b8cb426 Mon Sep 17 00:00:00 2001 From: javier-gracia-tabuenca-tuni <54809193+javier-gracia-tabuenca-tuni@users.noreply.github.com> Date: Fri, 20 Mar 2026 18:38:44 -0400 Subject: [PATCH 2/8] Update instructions for NEWS.md file updates Clarify instructions for updating the NEWS.md file, including versioning and summary requirements. --- .github/agents/my-agent.agent.md | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/agents/my-agent.agent.md b/.github/agents/my-agent.agent.md index a7460c7..4245fe8 100644 --- a/.github/agents/my-agent.agent.md +++ b/.github/agents/my-agent.agent.md @@ -43,6 +43,7 @@ The aim of this agent is to find what codes in the source tables do not exists i - ADD_INFO:sourceValidStartDate: Date in BeginningDate formated as YYYY-MM-DD or empty if it isempty in the source table. - ADD_INFO:sourceValidEndDate: Date in ExpiringDate formated as YYYY-MM-DD or empty if it is empty in the source table. - ADD_INFO:sourceParents: ParentId +5. Update the NEWS.md file for the target vocabulary in VOCABULARY//NEWS.md. Increase the number in the .. version tag. Summaryse in one line the changens introduced, including, number of additions and date. From 4b9fe0e11469ef32d350836a944d7c7016a7d89f Mon Sep 17 00:00:00 2001 From: javier-gracia-tabuenca-tuni <54809193+javier-gracia-tabuenca-tuni@users.noreply.github.com> Date: Mon, 23 Mar 2026 11:02:54 +0200 Subject: [PATCH 3/8] Modify sourceName assignment rule in agent documentation Updated the rule for sourceName assignment to include a translation fallback. --- .github/agents/my-agent.agent.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/agents/my-agent.agent.md b/.github/agents/my-agent.agent.md index 4245fe8..16d42c2 100644 --- a/.github/agents/my-agent.agent.md +++ b/.github/agents/my-agent.agent.md @@ -24,7 +24,7 @@ The aim of this agent is to find what codes in the source tables do not exists i 3. Find the rows from the source vocabulary with a CodeId that DO NOT exists in the target vocabulary table. 4. Take these codes found in previous step and append them to the target vocabulary table following this rules per each target column : - sourceCode: CodeId - - sourceName: A:Long_name + - sourceName: A:Long_name, If A:Long_name is empty, then take LongName, which is in Finnish and traslate it into English - sourceFrequency: 0 - matchScore: 0 - mappingStatus: UNCHECKED From fa743f00f260b6b1d849783cd58f9cbceb3ba649 Mon Sep 17 00:00:00 2001 From: javier-gracia-tabuenca-tuni <54809193+javier-gracia-tabuenca-tuni@users.noreply.github.com> Date: Mon, 23 Mar 2026 12:19:42 +0200 Subject: [PATCH 4/8] Revise instructions for sourceNames and NEWS.md update --- .github/agents/my-agent.agent.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/agents/my-agent.agent.md b/.github/agents/my-agent.agent.md index 16d42c2..1dbe84b 100644 --- a/.github/agents/my-agent.agent.md +++ b/.github/agents/my-agent.agent.md @@ -43,7 +43,8 @@ The aim of this agent is to find what codes in the source tables do not exists i - ADD_INFO:sourceValidStartDate: Date in BeginningDate formated as YYYY-MM-DD or empty if it isempty in the source table. - ADD_INFO:sourceValidEndDate: Date in ExpiringDate formated as YYYY-MM-DD or empty if it is empty in the source table. - ADD_INFO:sourceParents: ParentId -5. Update the NEWS.md file for the target vocabulary in VOCABULARY//NEWS.md. Increase the number in the .. version tag. Summaryse in one line the changens introduced, including, number of additions and date. +5. Make sure that for all the new rows the new sourceNames are in English and not if Finnish. If they are in Finnish translate them to English. +6. Update the NEWS.md file for the target vocabulary in VOCABULARY//NEWS.md. Increase the number in the .. version tag. Summaryse in one line the changens introduced, including, number of additions and date. From e4ec7d2790614ae55db833879295c40725293d18 Mon Sep 17 00:00:00 2001 From: javier-gracia-tabuenca-tuni <54809193+javier-gracia-tabuenca-tuni@users.noreply.github.com> Date: Tue, 24 Mar 2026 10:38:12 +0200 Subject: [PATCH 5/8] Create MainRelease agent for updating NEWS.md This agent updates the main NEWS.md by summarizing changes from vocabulary-specific NEWS.md files since the last main release. --- .github/agents/main-release.agent.md | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 .github/agents/main-release.agent.md diff --git a/.github/agents/main-release.agent.md b/.github/agents/main-release.agent.md new file mode 100644 index 0000000..c3d89e9 --- /dev/null +++ b/.github/agents/main-release.agent.md @@ -0,0 +1,19 @@ +--- +# Fill in the fields below to create a basic custom agent for your repository. +# The Copilot CLI can be used for local testing: https://gh.io/customagents/cli +# To make this agent available, merge this file into the default repository branch. +# For format details, see: https://gh.io/customagents/config + +name: MainRelease +description: Updates the main NEWS.md looking at each vocabualy NEWS.md +--- + +# Main Release NEWS.md Update +1. Look at the diffs between the development branch and the main brach for all the NEWS.md files in each of the vocabularies' folders +2. Use this diffs to create a summary of the changes for each vocabulary since the last main release +3. Update the root NEWS.md file by + - Bumping the major version + - Indicate the project update reason given in the issue that triggered this agent + - For each vocabulary that has an update, a summary of the updates + - Follow the format in the previous releases in the NEWS.md file + From 8d16f08bafb3e65ebb75d591ca00750dba792019 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Tue, 24 Mar 2026 08:40:26 +0000 Subject: [PATCH 6/8] Initial plan From 758de36fa391146eba641737de48fc393f4015f0 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Tue, 24 Mar 2026 08:51:02 +0000 Subject: [PATCH 7/8] Update NEWS.md for v4.0.0 main release Feb2026 --- NEWS.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/NEWS.md b/NEWS.md index 8078a09..a39666f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,19 @@ +# v4.0.0 +- Updated Athena vocabulary February 2026 +- Updated mappings for FGVisitType, ICD10fi, LABfi_ALL, NCSPfi, SPAT, UNITfi and VNRfi vocabularies +- FGVisitType: Added Spirometry visit and measurement codes with mappings; Source biobanks within Spirometry now have parent concept BIOBANK +- FGVisitType: Added seven drug registry source codes covering vaccination, rheuma, hospital administered and other drugs +- ICD10fi: Added 7 new codes from THL ICD-10 koodistopalvelu update +- LABfi_ALL: Major release for FinnGen DF14; source codes longer than 50 characters are now truncated +- NCSPfi: Added 362 new codes from NCSPfi 2026 March update; translated 305 Finnish sourceName values to English +- NCSPfi: Added 93 HUS imaging and 262 HUS heart operation codes mapped in PHEMS project +- NCSPfi: Fixed mapping of AA1AA from CT of head to Plain X-ray of head +- SPAT: Added 5 new SPAT codes (SPAT1416–SPAT1420) from koodistopalvelu update +- UNITfi: Minor fixes for FinnGen DF14 +- VNRfi: Added 239 new drugs, out of which 89 have been mapped; introduced dummy VNRs from 20 million range +- VNRfi: Dummy vaccination VNRs between 20000000 and 20000096 were mapped to ATC concept id + + # v3.0.0 - Updated Athena vocabulary August 2025 - Updated mappings for ICD8fi, ICD9fi, ICD10fi, NCSPfi, ICPC, LABfi, LABfi_ALL, MICROBEfi, MICROBEfi_TKU, SNOMED2fi and VNRfi vocabularies From 6dde4a1073f069bea3cf636ec6aaa03c3adff5f5 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Tue, 29 Sep 2026 05:33:07 +0000 Subject: [PATCH 8/8] Initial plan